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Hello everyone,
I am having trouble getting past the very first stages of trac-all -prep. I am using FreeSurfer 7.3.2. I tried several workarounds based on previous answers to similar problems in this mailing list, but I am unsuccessful each time.
First, when I try to run trac-all -prep without any configuration file, using only the defaults, it prints out an error:
trac-all -prep -s sub-01 -i $SUBJECTS_DIR/raw/sub-01/dwi/1_0000.dcm ERROR: for B0 distortion correction with reverse-polarity DWIs ERROR: or for model-based eddy-current distortion correction, ERROR: must specify PE direction
As I understand it, the default version of trac-all should assume default deb0=0, and not look for reverse-polarity images to do distortion correction for TOPUP.
Then, I tried to perform the analysis using the configuration file and specify that I do not want to perform correction based on reverse-polarity images or phase maps (my data don't have these), by explicitly entering "set dob0 = 0". The problem persisted. I did what a previous user was told to do - set "pedir" and "epifactor" and "echospacing" manually.
Then, I ran into the final error which I cannot overcome. No matter what I do, it ends in an error:
mv: cannot stat '/home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig_las.1.nii.gz': No such file or directory It seems it cannot create this file.
Earlier in the log there is also a previously mentioned error: INFO: input image orientation is LPS INFO: input image determinant is 6.49902 mri_convert -oni 128 -onj 128 -onk 60 -oid 0 0 0 -ojd 0 0 0 -okd 0 0 0 -oc 0 -21 7 -rt nearest /home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig.1.nii.gz /home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig_las.1.nii.gz mri_convert -oni 128 -onj 128 -onk 60 -oid 0 0 0 -ojd 0 0 0 -okd 0 0 0 -oc 0 -21 7 -rt nearest /home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig.1.nii.gz /home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig_las.1.nii.gz
mri_convert: directions must have non-zero magnitude; out_i_direction = (0, 0, 0)
It appears to be a problem with converting into LAS.
(Previously there was mention of there being a wrong "trac-preproc" file for runs with only 1 subject, but my problem remains when trying to run single and multiple subjects. I also tried to change my trac-preproc file to the versions from previous answers, with no luck).
When I check the dmri folder the dwi_orig.1.bvals and dwi_orig.1.bvecs, and dwi_orig_las.1.bvals files contain correct values, but dwi_orig_las.1.bvecs contains only zeros.
When I run mri_info on dwi_orig.1.nii.gz I get this:
Volume information for sub-01/dmri/dwi_orig.1.nii.gz type: nii dimensions: 128 x 128 x 60 x 76 voxel sizes: 1.718750, 1.718750, 2.200000 type: SHORT (4) fov: 220.000 dof: 1 xstart: -110.0, xend: 110.0 ystart: -110.0, yend: 110.0 zstart: -66.0, zend: 66.0 TR: 7100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 76 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9959, y_r = -0.0243, z_r = -0.0868, c_r = -0.4050 : x_a = 0.0326, y_a = -0.9949, z_a = -0.0955, c_a = -21.6846 : x_s = -0.0841, y_s = -0.0979, z_s = 0.9916, c_s = 7.5075 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.7117 -0.0418 -0.1910 117.5550 0.0561 -1.7100 -0.2100 90.4641 -0.1445 -0.1683 2.1816 -37.9249 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 6.49902
ras to voxel transform: -0.5794 0.0190 -0.0489 64.5443 -0.0142 -0.5789 -0.0570 51.8698 -0.0395 -0.0434 0.4507 25.6592 0.0000 0.0000 0.0000 1.0000
"PhEncDir" shows UNKNOWN, but as I said, my config file contains "set pedir = (AP)".
I also tried to do the analysis on FreeSurfer 7.2 and the develeopment version, but no luck.
I would appreciate any input into how to solve this problem.
Regards, SJ.